GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rhaP in Burkholderia phytofirmans PsJN

Align RhaP, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate BPHYT_RS25825 BPHYT_RS25825 ABC transporter permease

Query= TCDB::Q7BSH3
         (333 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS25825 BPHYT_RS25825 ABC
           transporter permease
          Length = 333

 Score =  192 bits (487), Expect = 1e-53
 Identities = 114/303 (37%), Positives = 177/303 (58%), Gaps = 4/303 (1%)

Query: 8   RETLLFLIIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTKSIDLSVA 67
           R   L+    +++VVFS  +  F +  N   I   T+++ I+A+    VI+ + IDLSV 
Sbjct: 34  RPYALYAAFAILLVVFSFASPWFLSIDNFLNIGRQTALVSIIAIGMTFVIIARQIDLSVG 93

Query: 68  ANLAFTGMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVVTLGTLT 127
           + LA +GM+ A+   A+     V+  +  +  GA +GAING +   + IP  +VTLGTL+
Sbjct: 94  STLALSGMSAALA-MAYVGNNWVIGAIAGIGTGAIVGAINGIVTTRVNIPSFLVTLGTLS 152

Query: 128 IYRGMAFVLSGGAWVNAHQMTPIFLSV-PRTPVLGLPVLSWVGIIIVILMYVLLRYTQFG 186
             RG+A +++    V     +  F+S+     + G+PV     ++ VI   +LL Y+ FG
Sbjct: 153 AARGLALMVTTTKPVIIDNDS--FISIFGEGDIFGVPVPIIWTLLAVIAGILLLHYSVFG 210

Query: 187 RSAYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIANGFELD 246
           R  YA GGNPTAA+Y+GI+T     LAF+L+G LAGLA+ +  +R   A  D+  G ELD
Sbjct: 211 RQIYAAGGNPTAALYSGINTRRVTTLAFILTGMLAGLAALVLSARSHAARPDVVQGMELD 270

Query: 247 SVAACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVIILAVAF 306
            +A+  +GG S+ GG G V GT+LG+L +G + N L ++G+S   Q+ I G +I+ AVAF
Sbjct: 271 VIASVTLGGCSLFGGRGFVLGTLLGSLIIGTLNNGLVLLGVSSSLQLVIKGVIIVAAVAF 330

Query: 307 NAR 309
             +
Sbjct: 331 TRK 333


Lambda     K      H
   0.328    0.141    0.413 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 270
Number of extensions: 15
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 333
Length of database: 333
Length adjustment: 28
Effective length of query: 305
Effective length of database: 305
Effective search space:    93025
Effective search space used:    93025
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory